/*=========================================================================
 *
 *  Copyright Insight Software Consortium
 *
 *  Licensed under the Apache License, Version 2.0 (the "License");
 *  you may not use this file except in compliance with the License.
 *  You may obtain a copy of the License at
 *
 *         http://www.apache.org/licenses/LICENSE-2.0.txt
 *
 *  Unless required by applicable law or agreed to in writing, software
 *  distributed under the License is distributed on an "AS IS" BASIS,
 *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 *  See the License for the specific language governing permissions and
 *  limitations under the License.
 *
 *=========================================================================*/
#ifndef itkResampleImageFilter_hxx
#define itkResampleImageFilter_hxx

#include "itkResampleImageFilter.h"
#include "itkObjectFactory.h"
#include "itkIdentityTransform.h"
#include "itkProgressReporter.h"
#include "itkImageRegionIteratorWithIndex.h"
#include "itkImageScanlineIterator.h"
#include "itkSpecialCoordinatesImage.h"
#include "itkDefaultConvertPixelTraits.h"

namespace itk
{
/**
 * Initialize new instance
 */
template <typename TInputImage,
          typename TOutputImage,
          typename TInterpolatorPrecisionType,
          typename TTransformPrecisionType>
ResampleImageFilter<TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType>::
  ResampleImageFilter()
{
  m_OutputOrigin.Fill(0.0);
  m_OutputSpacing.Fill(1.0);
  m_OutputDirection.SetIdentity();

  m_UseReferenceImage = false;

  m_Size.Fill(0);
  m_OutputStartIndex.Fill(0);

  // Pipeline input configuration

  // implicit:
  // #0 "Primary" required

  //  #1 "ReferenceImage" optional
  Self::AddRequiredInputName("ReferenceImage", 1);
  Self::RemoveRequiredInputName("ReferenceImage");

  //   "Transform" required ( not numbered )
  Self::AddRequiredInputName("Transform");
  Self::SetTransform(IdentityTransform<TTransformPrecisionType, ImageDimension>::New());

  m_Interpolator = dynamic_cast<InterpolatorType *>(LinearInterpolatorType::New().GetPointer());

  m_Extrapolator = nullptr;

  m_DefaultPixelValue = NumericTraits<PixelType>::ZeroValue(m_DefaultPixelValue);
}

/**
 * Print out a description of self
 *
 * \todo Add details about this class
 */
template <typename TInputImage,
          typename TOutputImage,
          typename TInterpolatorPrecisionType,
          typename TTransformPrecisionType>
void
ResampleImageFilter<TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType>::PrintSelf(
  std::ostream & os,
  Indent         indent) const
{
  Superclass::PrintSelf(os, indent);

  os << indent
     << "DefaultPixelValue: " << static_cast<typename NumericTraits<PixelType>::PrintType>(m_DefaultPixelValue)
     << std::endl;
  os << indent << "Size: " << m_Size << std::endl;
  os << indent << "OutputStartIndex: " << m_OutputStartIndex << std::endl;
  os << indent << "OutputSpacing: " << m_OutputSpacing << std::endl;
  os << indent << "OutputOrigin: " << m_OutputOrigin << std::endl;
  os << indent << "OutputDirection: " << m_OutputDirection << std::endl;
  os << indent << "Transform: " << this->GetTransform() << std::endl;
  os << indent << "Interpolator: " << m_Interpolator.GetPointer() << std::endl;
  os << indent << "Extrapolator: " << m_Extrapolator.GetPointer() << std::endl;
  os << indent << "UseReferenceImage: " << (m_UseReferenceImage ? "On" : "Off") << std::endl;
}

/**
 * Set the output image spacing.
 */
template <typename TInputImage,
          typename TOutputImage,
          typename TInterpolatorPrecisionType,
          typename TTransformPrecisionType>
void
ResampleImageFilter<TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType>::SetOutputSpacing(
  const double * spacing)
{
  SpacingType s;
  for (unsigned int i = 0; i < TOutputImage::ImageDimension; ++i)
  {
    s[i] = static_cast<typename SpacingType::ValueType>(spacing[i]);
  }
  this->SetOutputSpacing(s);
}

/**
 * Set the output image origin.
 */
template <typename TInputImage,
          typename TOutputImage,
          typename TInterpolatorPrecisionType,
          typename TTransformPrecisionType>
void
ResampleImageFilter<TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType>::SetOutputOrigin(
  const double * origin)
{
  OriginPointType p(origin);

  this->SetOutputOrigin(p);
}

/** Helper method to set the output parameters based on this image */
template <typename TInputImage,
          typename TOutputImage,
          typename TInterpolatorPrecisionType,
          typename TTransformPrecisionType>
void
ResampleImageFilter<TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType>::
  SetOutputParametersFromImage(const ImageBaseType * image)
{
  this->SetOutputOrigin(image->GetOrigin());
  this->SetOutputSpacing(image->GetSpacing());
  this->SetOutputDirection(image->GetDirection());
  this->SetOutputStartIndex(image->GetLargestPossibleRegion().GetIndex());
  this->SetSize(image->GetLargestPossibleRegion().GetSize());
}

/**
 * Set up state of filter before multi-threading.
 * InterpolatorType::SetInputImage is not thread-safe and hence
 * has to be set up before ThreadedGenerateData
 */
template <typename TInputImage,
          typename TOutputImage,
          typename TInterpolatorPrecisionType,
          typename TTransformPrecisionType>
void
ResampleImageFilter<TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType>::
  BeforeThreadedGenerateData()
{

  if (!m_Interpolator)
  {
    itkExceptionMacro(<< "Interpolator not set");
  }

  // Connect input image to interpolator
  m_Interpolator->SetInputImage(this->GetInput());

  // Connect input image to extrapolator
  if (!m_Extrapolator.IsNull())
  {
    m_Extrapolator->SetInputImage(this->GetInput());
  }

  unsigned int nComponents = DefaultConvertPixelTraits<PixelType>::GetNumberOfComponents(m_DefaultPixelValue);

  if (nComponents == 0)
  {
    PixelComponentType zeroComponent = NumericTraits<PixelComponentType>::ZeroValue(zeroComponent);
    nComponents = this->GetInput()->GetNumberOfComponentsPerPixel();
    NumericTraits<PixelType>::SetLength(m_DefaultPixelValue, nComponents);
    for (unsigned int n = 0; n < nComponents; n++)
    {
      PixelConvertType::SetNthComponent(n, m_DefaultPixelValue, zeroComponent);
    }
  }
}

/**
 * Set up state of filter after multi-threading.
 */
template <typename TInputImage,
          typename TOutputImage,
          typename TInterpolatorPrecisionType,
          typename TTransformPrecisionType>
void
ResampleImageFilter<TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType>::
  AfterThreadedGenerateData()
{
  // Disconnect input image from the interpolator
  m_Interpolator->SetInputImage(nullptr);
  if (!m_Extrapolator.IsNull())
  {
    // Disconnect input image from the extrapolator
    m_Extrapolator->SetInputImage(nullptr);
  }
}

/**
 * ThreadedGenerateData
 */
template <typename TInputImage,
          typename TOutputImage,
          typename TInterpolatorPrecisionType,
          typename TTransformPrecisionType>
void
ResampleImageFilter<TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType>::
  ThreadedGenerateData(const OutputImageRegionType & outputRegionForThread, ThreadIdType threadId)
{
  // Check whether the input or the output is a
  // SpecialCoordinatesImage.  If either are, then we cannot use the
  // fast path since index mapping will definitely not be linear.
  using OutputSpecialCoordinatesImageType = SpecialCoordinatesImage<PixelType, ImageDimension>;
  using InputSpecialCoordinatesImageType = SpecialCoordinatesImage<InputPixelType, InputImageDimension>;

  const bool isSpecialCoordinatesImage = (dynamic_cast<const InputSpecialCoordinatesImageType *>(this->GetInput()) ||
                                          dynamic_cast<const OutputSpecialCoordinatesImageType *>(this->GetOutput()));

  // Check whether we can use a fast path for resampling. Fast path
  // can be used if the transformation is linear. Transform respond
  // to the IsLinear() call.
  if (!isSpecialCoordinatesImage && this->GetTransform()->GetTransformCategory() == TransformType::Linear)
  {
    this->LinearThreadedGenerateData(outputRegionForThread, threadId);
    return;
  }

  // Otherwise, we use the normal method where the transform is called
  // for computing the transformation of every point.
  this->NonlinearThreadedGenerateData(outputRegionForThread, threadId);
}

/**
 * Cast from interpolotor output to pixel type
 */
template <typename TInputImage,
          typename TOutputImage,
          typename TInterpolatorPrecisionType,
          typename TTransformPrecisionType>
typename ResampleImageFilter<TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType>::PixelType
ResampleImageFilter<TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType>::
  CastPixelWithBoundsChecking(const InterpolatorOutputType value,
                              const ComponentType          minComponent,
                              const ComponentType          maxComponent) const
{
  const unsigned int nComponents = InterpolatorConvertType::GetNumberOfComponents(value);
  PixelType          outputValue;

  NumericTraits<PixelType>::SetLength(outputValue, nComponents);

  for (unsigned int n = 0; n < nComponents; n++)
  {
    ComponentType component = InterpolatorConvertType::GetNthComponent(n, value);

    if (component < minComponent)
    {
      PixelConvertType::SetNthComponent(n, outputValue, static_cast<PixelComponentType>(minComponent));
    }
    else if (component > maxComponent)
    {
      PixelConvertType::SetNthComponent(n, outputValue, static_cast<PixelComponentType>(maxComponent));
    }
    else
    {
      PixelConvertType::SetNthComponent(n, outputValue, static_cast<PixelComponentType>(component));
    }
  }

  return outputValue;
}

/**
 * NonlinearThreadedGenerateData
 */
template <typename TInputImage,
          typename TOutputImage,
          typename TInterpolatorPrecisionType,
          typename TTransformPrecisionType>
void
ResampleImageFilter<TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType>::
  NonlinearThreadedGenerateData(const OutputImageRegionType & outputRegionForThread, ThreadIdType threadId)
{
  // Get the output pointers
  OutputImageType * outputPtr = this->GetOutput();

  // Get this input pointers
  const InputImageType * inputPtr = this->GetInput();

  // Honor the SpecialCoordinatesImage isInside value returned
  // by TransformPhysicalPointToContinuousIndex
  using InputSpecialCoordinatesImageType = SpecialCoordinatesImage<InputPixelType, InputImageDimension>;
  const bool isSpecialCoordinatesImage = dynamic_cast<const InputSpecialCoordinatesImageType *>(inputPtr);

  // Get the input transform
  const TransformType * transformPtr = this->GetTransform();


  // Create an iterator that will walk the output region for this thread.
  using OutputIterator = ImageRegionIteratorWithIndex<TOutputImage>;
  OutputIterator outIt(outputPtr, outputRegionForThread);

  // Define a few indices that will be used to translate from an input pixel
  // to an output pixel
  PointType outputPoint; // Coordinates of current output pixel
  PointType inputPoint;  // Coordinates of current input pixel

  ContinuousInputIndexType inputIndex;

  // Support for progress methods/callbacks
  ProgressReporter progress(this, threadId, outputRegionForThread.GetNumberOfPixels());

  // Min/max values of the output pixel type AND these values
  // represented as the output type of the interpolator
  const PixelComponentType minValue = NumericTraits<PixelComponentType>::NonpositiveMin();
  const PixelComponentType maxValue = NumericTraits<PixelComponentType>::max();

  using OutputType = typename InterpolatorType::OutputType;
  const ComponentType minOutputValue = static_cast<ComponentType>(minValue);
  const ComponentType maxOutputValue = static_cast<ComponentType>(maxValue);

  // Walk the output region
  outIt.GoToBegin();

  while (!outIt.IsAtEnd())
  {
    // Determine the index of the current output pixel
    outputPtr->TransformIndexToPhysicalPoint(outIt.GetIndex(), outputPoint);

    // Compute corresponding input pixel position
    inputPoint = transformPtr->TransformPoint(outputPoint);
    const bool isInsideInput = inputPtr->TransformPhysicalPointToContinuousIndex(inputPoint, inputIndex);

    PixelType  pixval;
    OutputType value;
    // Evaluate input at right position and copy to the output
    if (m_Interpolator->IsInsideBuffer(inputIndex) && (!isSpecialCoordinatesImage || isInsideInput))
    {
      value = m_Interpolator->EvaluateAtContinuousIndex(inputIndex);
      pixval = this->CastPixelWithBoundsChecking(value, minOutputValue, maxOutputValue);
      outIt.Set(pixval);
    }
    else
    {
      if (m_Extrapolator.IsNull())
      {
        outIt.Set(m_DefaultPixelValue); // default background value
      }
      else
      {
        value = m_Extrapolator->EvaluateAtContinuousIndex(inputIndex);
        pixval = this->CastPixelWithBoundsChecking(value, minOutputValue, maxOutputValue);
        outIt.Set(pixval);
      }
    }

    progress.CompletedPixel();
    ++outIt;
  }
}


/**
 * LinearThreadedGenerateData
 */
template <typename TInputImage,
          typename TOutputImage,
          typename TInterpolatorPrecisionType,
          typename TTransformPrecisionType>
void
ResampleImageFilter<TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType>::
  LinearThreadedGenerateData(const OutputImageRegionType & outputRegionForThread, ThreadIdType threadId)
{
  // Get the output pointers
  OutputImageType * outputPtr = this->GetOutput();

  // Get this input pointers
  const InputImageType * inputPtr = this->GetInput();

  // Get the input transform
  const TransformType * transformPtr = this->GetTransform();

  // Create an iterator that will walk the output region for this thread.
  using OutputIterator = ImageScanlineIterator<TOutputImage>;

  OutputIterator outIt(outputPtr, outputRegionForThread);

  // Define a few indices that will be used to translate from an input pixel
  // to an output pixel
  PointType outputPoint; // Coordinates of current output pixel
  PointType inputPoint;  // Coordinates of current input pixel
  PointType tmpOutputPoint;
  PointType tmpInputPoint;

  ContinuousInputIndexType inputIndex;
  ContinuousInputIndexType tmpInputIndex;

  using VectorType = typename PointType::VectorType;
  VectorType delta; // delta in input continuous index coordinate frame

  IndexType index;

  const typename OutputImageRegionType::SizeType & regionSize = outputRegionForThread.GetSize();
  const SizeValueType numberOfLinesToProcess = outputRegionForThread.GetNumberOfPixels() / regionSize[0];

  // Support for progress methods/callbacks
  ProgressReporter progress(this, threadId, numberOfLinesToProcess);

  using OutputType = typename InterpolatorType::OutputType;

  // Cache information from the superclass
  PixelType defaultValue = this->GetDefaultPixelValue();

  // Min/max values of the output pixel type AND these values
  // represented as the output type of the interpolator
  const PixelComponentType minValue = NumericTraits<PixelComponentType>::NonpositiveMin();
  const PixelComponentType maxValue = NumericTraits<PixelComponentType>::max();

  using OutputType = typename InterpolatorType::OutputType;
  const ComponentType minOutputValue = static_cast<ComponentType>(minValue);
  const ComponentType maxOutputValue = static_cast<ComponentType>(maxValue);

  // Determine the position of the first pixel in the scanline
  index = outIt.GetIndex();
  outputPtr->TransformIndexToPhysicalPoint(index, outputPoint);

  // Compute corresponding input pixel position
  inputPoint = transformPtr->TransformPoint(outputPoint);
  inputPtr->TransformPhysicalPointToContinuousIndex(inputPoint, inputIndex);

  // As we walk across a scan line in the output image, we trace
  // an oriented/scaled/translated line in the input image.  Cache
  // the delta along this line in continuous index space of the input
  // image. This allows us to use vector addition to model the
  // transformation.
  //
  // To find delta, we take two pixels adjacent in a scanline
  // and determine the continuous indices of these pixels when
  // mapped to the input coordinate frame. We use the difference
  // between these two continuous indices as the delta to apply
  // to an index to trace line in the input image as we move
  // across the scanline of the output image.
  //
  // We determine delta in this manner so that Images
  // are both handled properly (taking into account the direction cosines).
  //
  ++index[0];
  outputPtr->TransformIndexToPhysicalPoint(index, tmpOutputPoint);
  tmpInputPoint = transformPtr->TransformPoint(tmpOutputPoint);
  inputPtr->TransformPhysicalPointToContinuousIndex(tmpInputPoint, tmpInputIndex);
  delta = tmpInputIndex - inputIndex;

  while (!outIt.IsAtEnd())
  {
    // Determine the continuous index of the first pixel of output
    // scanline when mapped to the input coordinate frame.
    //

    // First get the position of the pixel in the output coordinate frame
    index = outIt.GetIndex();
    outputPtr->TransformIndexToPhysicalPoint(index, outputPoint);

    // Compute corresponding input pixel continuous index, this index
    // will incremented in the scanline loop
    inputPoint = transformPtr->TransformPoint(outputPoint);
    inputPtr->TransformPhysicalPointToContinuousIndex(inputPoint, inputIndex);

    while (!outIt.IsAtEndOfLine())
    {
      PixelType  pixval;
      OutputType value;
      // Evaluate input at right position and copy to the output
      if (m_Interpolator->IsInsideBuffer(inputIndex))
      {
        value = m_Interpolator->EvaluateAtContinuousIndex(inputIndex);
        pixval = this->CastPixelWithBoundsChecking(value, minOutputValue, maxOutputValue);
        outIt.Set(pixval);
      }
      else
      {
        if (m_Extrapolator.IsNull())
        {
          outIt.Set(defaultValue); // default background value
        }
        else
        {
          value = m_Extrapolator->EvaluateAtContinuousIndex(inputIndex);
          pixval = this->CastPixelWithBoundsChecking(value, minOutputValue, maxOutputValue);
          outIt.Set(pixval);
        }
      }

      ++outIt;
      inputIndex += delta;
    }
    progress.CompletedPixel();
    outIt.NextLine();
  } // while( !outIt.IsAtEnd() )
}

/**
 * Inform pipeline of necessary input image region
 *
 * Determining the actual input region is non-trivial, especially
 * when we cannot assume anything about the transform being used.
 * So we do the easy thing and request the entire input image.
 */
template <typename TInputImage,
          typename TOutputImage,
          typename TInterpolatorPrecisionType,
          typename TTransformPrecisionType>
void
ResampleImageFilter<TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType>::
  GenerateInputRequestedRegion()
{
  // call the superclass's implementation of this method
  Superclass::GenerateInputRequestedRegion();

  if (!this->GetInput())
  {
    return;
  }

  // get pointers to the input and output
  InputImagePointer inputPtr = const_cast<TInputImage *>(this->GetInput());

  // Request the entire input image
  inputPtr->SetRequestedRegionToLargestPossibleRegion();
}

/**
 * Inform pipeline of required output region
 */
template <typename TInputImage,
          typename TOutputImage,
          typename TInterpolatorPrecisionType,
          typename TTransformPrecisionType>
void
ResampleImageFilter<TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType>::
  GenerateOutputInformation()
{
  // call the superclass' implementation of this method
  Superclass::GenerateOutputInformation();

  // get pointers to the input and output
  OutputImageType * outputPtr = this->GetOutput();
  if (!outputPtr)
  {
    return;
  }

  const ReferenceImageBaseType * referenceImage = this->GetReferenceImage();

  // Set the size of the output region
  if (m_UseReferenceImage && referenceImage)
  {
    outputPtr->SetLargestPossibleRegion(referenceImage->GetLargestPossibleRegion());
  }
  else
  {
    typename TOutputImage::RegionType outputLargestPossibleRegion;
    outputLargestPossibleRegion.SetSize(m_Size);
    outputLargestPossibleRegion.SetIndex(m_OutputStartIndex);
    outputPtr->SetLargestPossibleRegion(outputLargestPossibleRegion);
  }

  // Set spacing and origin
  if (m_UseReferenceImage && referenceImage)
  {
    outputPtr->SetSpacing(referenceImage->GetSpacing());
    outputPtr->SetOrigin(referenceImage->GetOrigin());
    outputPtr->SetDirection(referenceImage->GetDirection());
  }
  else
  {
    outputPtr->SetSpacing(m_OutputSpacing);
    outputPtr->SetOrigin(m_OutputOrigin);
    outputPtr->SetDirection(m_OutputDirection);
  }
}

/**
 * Verify if any of the components has been modified.
 */
template <typename TInputImage,
          typename TOutputImage,
          typename TInterpolatorPrecisionType,
          typename TTransformPrecisionType>
ModifiedTimeType
ResampleImageFilter<TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType>::GetMTime(
  void) const
{
  ModifiedTimeType latestTime = Object::GetMTime();

  if (m_Interpolator)
  {
    if (latestTime < m_Interpolator->GetMTime())
    {
      latestTime = m_Interpolator->GetMTime();
    }
  }

  return latestTime;
}

} // end namespace itk

#endif
